Proteins 2

• Peptide


  A molecule containing 2 or more amino acids
• Protein


  Made up of one or more polypeptides arranged in a biologically functional way
• Peptides


  • Contain approximately 50 amino acids or less
• Proteins


  • May be bound to ligands, another protein or other macromolecule, or complex macromolecular assemblies
• Peptide


  • Dipeptide (2 amino acids)
  • Tripeptide (3 amino acids)
  • Tetrapeptide (4 amino acids)
  • Octapeptide (8 amino acids)
  • Oligopeptide (a few, up to 20 amino acids)
• Polypeptide


  More than 50 amino acids (long continuous unbranched peptide chain)
• 1. terminal


  First amino acid
• 1. terminal


  Last amino acid
• Naming the peptide


  1. Order of amino acids in a peptide: Left (N-terminal a.a.) is written first, C-terminal next

  2. Naming of polypeptides: Component a.a. in peptides called moieties or residues, except for C-terminal which is called -ine, -ate, or -ic
• Classification of Proteins


  • Based on composition: Simple proteins, Conjugated proteins (lipoproteins, glycoproteins, metalloproteins, hemoproteins, flavoproteins)
  • Based on shape and solubility: Fibrous, Globular, Membrane
• Simple proteins


  • Yield only amino acids when hydrolyzed
• Conjugated proteins


  • Yield amino acids and non-amino acid components called prosthetic groups
• Conjugated proteins


  • Lipoproteins (lipid)
  • Glycoproteins (carbohydrate)
  • Metalloproteins (Cu, Fe, Zn, Mo)
  • Hemoproteins (heme)
  • Flavoproteins (flavin nucleotide)
• Fibrous proteins


  • Elongated, straight or twisted, generally insoluble, mainly structural function, consist largely of a single type of 2D structure (e.g. α-keratin, collagen, silk fibroin)
• Globular proteins


  • Compact, highly ordered pattern of folding, soluble and have dynamic cellular functions (e.g. enzymes, hormones), often contain several types of 2D structure (e.g. albumin, globulin, haemoglobin, enzymes)
• Membrane proteins


  • Hydrophilic aa side chains oriented outward, water insoluble, found associated with various membrane systems of cells
• Functions of Proteins


  • Catalysis (enzymes)
  • Regulation (repressors, activators, hormones)
  • Defense (antibodies, fibrinogen)
  • Structural (collagen, elastin, keratin)
  • Movement (actin, myosin)
  • Transport (albumin, haemoglobin)
  • Storage (casein, ovalbumin, legumin, vicelin, prolamines)
  • Communication (membrane proteins)
  • Signal transduction
• Monomeric protein


  A single polypeptide chain
• Multimeric protein


  More than one polypeptide chain
• Multimeric proteins


  • Homomultimeric (all chains are the same)
  • Heteromultimeric (different chains)
• Conformation of proteins


  Spatial arrangement of all the atoms in a molecule
• Primary structure


  Linear sequence of the amino acids
• Secondary structure


  Initial folding of a polypeptide chain into shapes stabilized by hydrogen bonding between NH and CO groups, most common are Alpha helix & Beta pleated sheets
• Tertiary structure


  1. D arrangement of all the atoms in the protein, folded globular structure
• Quaternary structure


  Association & interaction of subunits in a multimeric protein
• Bonds in proteins


  • Covalent bonds (peptide bonds, disulfide bonds)
  • Noncovalent bonds (hydrophobic forces, hydrogen bonds, ionic bonds)
• Primary structure


  Sequence of amino acids
• Genetic diseases result from proteins with abnormal sequences
• Insulin


  2 polypeptide chains, 51 aa (subunit A=21 aa, subunit B=30 aa), two disulfide bridges
• Alpha-helix


  • Tightly packed and right-handed helix wound around an imaginary axis, 3.6 residues per turn, hydrogen bonds parallel to the direction of the helix axis, side chains stick out from helix
• Beta-pleated sheet


  • Perpendicular hydrogen bonds between peptide bond atoms, amino acid side chains alternate above and below the plane of the pleated sheet
• Polarity of the side chains


  Play an important role in protein folding and function
• Tertiary structure


  Folded globular structure, distant amino acids in the 1o structure may be brought close together, water-soluble proteins fold with nonpolar side-chains to the inside (hydrophobic core), stabilized by non-covalent associations and disulfide bonds
• Myoglobin


  Contains about 80% alpha-helix secondary structure, devoid of beta-sheet structure
• Hemoglobin


  Consist of more than one polypeptide chain (subunit), subunits interact via non-covalent bonds (H-bonds, electrostatic, hydrophobic)
• Denaturation of proteins


  Changes the three-dimensional structure, noncovalent bonds and disulfide bonds are broken but not the peptide bond backbone, primary structure remains intact
• Methods for isolation and separation of proteins


  • 1D gel electrophoresis (1D-E)
  • 2D gel electrophoresis (2D-E)
  • Protein Digestion
  • Purification
  • Isotope-Coded Affinity Tags (ICAT)